British scientists have developed a method of allele-specific probe polymerase chain reaction to detect various options or lines of origin of the coronavirus SARS-COV-2 in samples taken from the nasopharynx. It is reported by RIA Novosti with reference to the results of the study, published on the preprints of MedRxiv.org.
It is noted that the new method of quantitative polymerase chain reaction (PCR) allows you to detect virus versions in real time even in samples with a destroyed viral RNA. The gold standard for the detection of viral variants is considered to be methods of complete generation sequencing (NGS), but samples for these methods must have good quality and high levels of viral RNA, in addition NGS methods are expensive and not available for mass use.
Scientists used a new method, which they called allele-specific probe PCR, to detect viral versions in 717 samples taken in patients infected with SARS-COV-2, in the UK, as well as in 365 samples from Brazil.
According to data, in the first case, they found in the virus s-protein Mutation D1118H, characteristic of the alpha option, and in the second – K417T and L3468V mutations, characteristic of gamma-option coronavirus.
It is reported that for both cases they compared the sensitivity of allel-specific probe PCR with NGS methods.
The result showed that at 99% of the comparability of the detected virus options, the accuracy of the new method in samples with a wide range of virus loads by 25 percent is higher. It also effectively identified 95% of samples with destroyed RNA, while NGS methods can be sequenced by no more than 11% of degraded samples.
The new method showed 98% sensitivity and 100% specificity for the alpha variant. For the gamma variant, these parameters amounted to 90-95 and 91-100%, respectively.
Another advantage of the developed method is a light modification for targeting new mutations arising in the SARS-COV-2 genome in the future, which is very important for the operational tracking of the spread of new strains of coronavirus.